Some luthiers demonstrate that their bolt-on necked guitars can hang together without the bolts being inserted. I think this more an attempt at showcasing/showboating carpentry skills than musical instrument building skills, personally. Conversely a lot of highly coveted pre-CBS-era Fender instruments have visible gaps either side of the neck, big enough to get a guitar pick, if not several, into.
Ultimately I think it is a matter of personal taste. You can cook up a legitimate-sounding pseudo-scientific reason for both a tight and a loose neck pocket. After all, a lot of guitarists and luthiers think nothing of inserting a folded up piece of sand paper or bus ticket into a neck pocket to 'shim' a neck. This instantly breaks the solid wood-to-wood joint being made in the neck pocket. Moreover I've seen numerous Fenders with that finish crack in the body around the heel of the neck, indicative that perhaps the geometry of the neck heel or neck pocket has altered over time and cracked the finish. Does then a loose neck pocket allow for wider variation in climate without the risk of harming the finish, or does a tight neck-to-body join provide a robust barrier to moisture ingress, preserving the structural integrity of the instrument overall? And what impact does this have on the perceived tone of the instrument? Will your audience notice?
The legendary tone-chasing guitarist Eric Johnson claims he can hear different battery manufacturers when he uses their products to power his fuzz pedals. He also angles his fuzz pedals carefully in or out of alignment with his other pedals as he feels this is also important to the tone of them. Finally he likes to remove the finish on the bodies of his Strats where the bridge is mounted, to provide a rawer bridge-to-wood coupling, again in the name of tone. Reckon you would find folded up bus tickets in the neck pockets in his Strats? Reckon he will have a strong opinion on shimming necks?
This is all, unfortunately, a matter of personal opinion, and the science just isn't there, either way. I wouldn't use epoxy or filler material as you never know when that neck might have to be removed! Consider using threaded inserts to get a solid neck-to-body join, but consider also that you need a drill press, this is a destructive modification, and you need to measure twice and drill once!